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annotate tn93_filter.xml @ 0:9a790fb42c79 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
author iuc
date Fri, 23 Apr 2021 03:02:30 +0000
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children cc37e773d592
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9a790fb42c79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
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1 <tool id="tn93_filter" name="TN93 Filter" version="@VERSION@">
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2 <description>- remove sequences from a reference that are within a given distance of of a cluster</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
9a790fb42c79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
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6 <requirements>
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7 <requirement type="package" version="@VERSION@">tn93</requirement>
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8 <requirement type="package" version="1.70">biopython</requirement>
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9 </requirements>
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10 <version_command><![CDATA[tn93 --version]]></version_command>
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11 <command detect_errors="exit_code"><![CDATA[
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12 cat '$reads' > filtered_msa.fa &&
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13 tn93 -o pairwise.csv -s filtered_msa.fa -t $threshold '$clusters' &&
9a790fb42c79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
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14 python '$__tool_directory__/tn93_filter.py' --reference '$reference'
9a790fb42c79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
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15 --distances pairwise.csv
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16 --reads filtered_msa.fa
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17 --clusters '$clusters'
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18 ]]></command>
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19 <inputs>
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20 <param name="reads" type="data" format="fasta" label="Aligned reads" />
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21 <param name="reference" type="data" format="fasta" label="Reference sequence" />
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22 <param name="clusters" type="data" format="fasta" label="FASTA file with compressed clusters" />
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23 <param name="threshold" type="float" value="0.015" label="Pairwise distance threshold" />
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24 </inputs>
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25 <outputs>
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26 <data name="filtered_reference" format="fasta" from_work_dir="filtered_msa.fa" />
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27 </outputs>
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28 <tests>
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29 <test>
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30 <param name="reads" value="filter-in1-reads.fa" />
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31 <param name="reference" value="filter-in1-reference.fa" />
9a790fb42c79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
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32 <param name="clusters" value="filter-in1-clusters.fa" />
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33 <param name="threshold" value="0.35" />
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34 <output name="filtered_reference" file="filter-out1.fasta" ftype="fasta" />
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35 </test>
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36 </tests>
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37 <help><![CDATA[
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38 TN93-Filter
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39 ===========
9a790fb42c79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
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40
9a790fb42c79 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/tn93/ commit eec640a7c26b728f8175885926fe368b0756d9e5"
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41 Removes aligned sequences that are within a given distance from a reference
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42 sequence using the 1993 Tamura-Nei distance calculation.
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43 ]]></help>
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44 <expand macro="citations">
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45 <citation type="doi">10.1093/oxfordjournals.molbev.a040023</citation>
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46 </expand>
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47 </tool>